Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision

Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins

(2020) Joseph Dopie et al.   JOURNAL OF CELL BIOLOGY

Biomolecular Condensates in the Nucleus

(2020) Benjamin R. Sabari et al.   TRENDS IN BIOCHEMICAL SCIENCES

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

SON and SRRM2 are essential for nuclear speckle formation

(2020) İbrahim Avşar Ilik et al.   eLife

Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition

(2019) Jiah Kim et al.   JOURNAL OF CELL SCIENCE

Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome

(2019) Nicolas Viphakone et al.   MOLECULAR CELL

Constitutive splicing and economies of scale in gene expression

(2019) Fangyuan Ding et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome organization around nuclear speckles

(2019) Yu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler et al.   MOLECULAR CELL

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

(2018) Lydia Herzel et al.   GENOME RESEARCH

Balance between MAT2A intron detention and splicing is determined cotranscriptionally

(2018) Kathryn E. Pendleton et al.   RNA

Intronless mRNAs transit through nuclear speckles to gain export competence

(2018) Ke Wang et al.   JOURNAL OF CELL BIOLOGY

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

(2018) Alexander F. Palazzo et al.   Frontiers in Genetics

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

(2017) Hagen Tilgner et al.   GENOME RESEARCH

Cellular differentiation state modulates the mRNA export activity of SR proteins

(2017) Valentina Botti et al.   JOURNAL OF CELL BIOLOGY

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

(2017) Jingyi Fei et al.   JOURNAL OF CELL SCIENCE

SR Proteins: Binders, Regulators, and Connectors of RNA

(2017) Sunjoo Jeong   MOLECULES AND CELLS

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread intra-dependencies in the removal of introns from human transcripts

(2017) Seong Won Kim et al.   NUCLEIC ACIDS RESEARCH

Nuclear speckles: molecular organization, biological function and role in disease

(2017) Lukasz Galganski et al.   NUCLEIC ACIDS RESEARCH

Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm

(2017) Mattia Brugiolo et al.   NUCLEIC ACIDS RESEARCH

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture

(2017) Athma A Pai et al.   eLife

Droplet organelles?

(2016) Edward M Courchaine et al.   EMBO JOURNAL

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

(2016) Michaela Müller-McNicoll et al.   GENES & DEVELOPMENT

Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts

(2016) Nicola Meola et al.   MOLECULAR CELL

Targeted Intron Retention and Excision for Rapid Gene Regulation in Response to Neuronal Activity

(2016) Oriane Mauger et al.   NEURON

Global intron retention mediated gene regulation during CD4+T cell activation

(2016) Ting Ni et al.   NUCLEIC ACIDS RESEARCH

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

(2016) Allison Piovesan et al.   Database-The Journal of Biological Databases and Curation

Influenza virus mRNA trafficking through host nuclear speckles

(2016) Amir Mor et al.   Nature Microbiology

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

(2015) Paul L. Boutz et al.   GENES & DEVELOPMENT

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

(2015) Harold Pimentel et al.   NUCLEIC ACIDS RESEARCH

Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs

(2015) Stefan M. Bresson et al.   PLoS Genetics

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Sumoylation and transcription regulation at nuclear pores

(2014) Lorane Texari et al.   CHROMOSOMA

HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation

(2014) Nimish Khanna et al.   CURRENT BIOLOGY

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Inhibition of U4 snRNA in Human Cells Causes the Stable Retention of Polyadenylated Pre-mRNA in the Nucleus

(2014) Anne Hett et al.   PLoS One

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

(2014) Reut Shalgi et al.   Cell Reports

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

Promoter- and RNA polymerase II–dependenthsp-16gene association with nuclear pores inCaenorhabditis elegans

(2013) Sabine Rohner et al.   JOURNAL OF CELL BIOLOGY

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Co-transcriptional degradation of aberrant pre-mRNA by Xrn2

(2012) Lee Davidson et al.   EMBO JOURNAL

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

(2012) K. Yap et al.   GENES & DEVELOPMENT

SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles

(2012) Vidisha Tripathi et al.   MOLECULAR BIOLOGY OF THE CELL

Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion

(2012) Cyrille Girard et al.   Nature Communications

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult

(2012) Bin Zhang et al.   Cell Reports

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor

(2011) Kensuke Ninomiya et al.   JOURNAL OF CELL BIOLOGY

Son Is Essential for Nuclear Speckle Organization and Cell Cycle Progression

(2010) Alok Sharma et al.   MOLECULAR BIOLOGY OF THE CELL

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

A role for TREX components in the release of spliced mRNA from nuclear speckle domains

(2010) Anusha P. Dias et al.   Nature Communications